(1) It is less intrusive. Flow's type system is built on annotations which are simply stripped away at runtime (as opposed to writing in another - albeit similar - language that gets transpiled to JS. Sure the transformations are always "file-local" as TS folks say but still it is another, totally unecessary level of abstraction and transpilation.
(2) Flow's type system is at least equally and quite possibly much more expressive and nuanced than TS.
(3) Flow annotations can be applied in a much more piece-meal way than TS.
(4) zero issues integrating with 3rd party libraries (because of 1) - and that includes the ability to type-check said 3rd party libraries (which is a breeze with flow-typed)
(5) To take advantage of TS you have to write JS code in the "JS with classes" style (a.k.a "JS for C# coders"). In contrast Flow allows you to take advantage of its type checking while coding: (a) in idiomatic JS (prototypes) (b) in JS with classes (c) any combination and mix of the two approaches. Flow feels a lot less opinioned as to your JS programming style.
(6) Flow it is not coming from microsoft (but hey, don't you know we've changed, please give us another chance and we won't fuck you over this time, please we love you so). TS team is trying very hard (perhaps too hard) to distance themselves from the negative brand value of microsoft
(7) Flow is not a blueprint for the Mother of all embrace-extend-extigunish strategies (see #6).